|
System/Platform
|
Reaction Method
|
Pro
|
Con
|
Vendor
|
Relative Cost *
|
|
Luminex, Bio-Plex
|
ASPE (see figure), SBE, OLA |
• Choice of chemistries for PCR
• Multiplexing capability (up to 50-plex), especially for multiple variants from the same gene |
• Optimization may be difficult
• Requires dedicated instrument |
Luminex, Bio-Rad |
$$ |
|
Molecular inversion probes & GeneChip
|
Probe hybridization |
• Ideal for genome-wide studies
• Can be customized for smaller projects
• Can be outsourced |
• Without outsourcing, requires costly capital investment |
Affymetrix |
$ |
|
GoldenGate & BeadArray
|
ASPE & OLA |
Illumina |
$ |
|
Infinium II & BeadArray
|
ASPE / SBE |
Illumina |
$ |
|
TaqMan
|
FRET (see figure) |
• Highly specific and sensitive
• Simple closed-tube procedure |
• Limited multiplexing
• Relatively costly |
Applied Biosystems |
$$$ |
|
High-resolution melting-curve analysis
|
Intercalating dye, hybridization probe (labeled or unlabeled) |
• Rapid, inexpensive, suitable for multiplex assays and for simultaneous screening of unknown variants
• No variant-specific primer or probes
• Simple closed-tube procedure |
• May miss some variants in lower resolution platforms
• Nonspecific amplification may interfere (but easy to rule out) |
Idaho Technology, Roche Applied Science |
$ |
|
MassArray
|
SBE (hME or iPLEX) |
• Ultrahigh throughput and multiplexing with small amount of DNA
• No labeling
• Automated allele calling |
• Expensive dedicated equipment required |
Sequenom |
$ |
|
Pyrosequencing
|
SBE & luminescence (see figure) |
• Quantitative allele signal (suitability for DNA pooling studies)
• Most suitable for multiplexing for closely spaced variants within 50 bases |
• Limited multiplexing for independent variants
• Relatively high cost for dedicated equipment
• Relatively costly assay |
Biotage |
$$$ |
|
SNPstream
|
SBE |
48-plex assays |
• Complicated multistep procedure and not closed-tube
• Not suitable for all variants
• Requires a genetic analyzer (capillary electrophoresis) |
Orchid Biosciences, Beckman Coulter |
$$ |
|
SNaPshot
|
SBE |
10-plex assays |
Applied Biosystems |
$$ |
|
SNPlex
|
OLA |
48-plex assays |
Applied Biosystems |
$$ |
| ASPE: allele-specific primer extension; SBE: single-base extension; OLA: oligonucleotide ligation assay; FRET: fluorescence resonance energy transfer; hME: homogeneous Mass EXTENT (single to 4-plex assay); iPLEX: Sequenom chemistry for up to 29-plex level). |
| * Cost per variant and excluding capital equipment cost |
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